Dear Eclipse Community,
I know there is a tremendous amount of information online, and StackOverflow full of Eclipse-RCP questions already. But the downside of that is that there is a lot of noise. Would it be an idea to set up a StackExchange dedicated to development of Eclipse RCP-based applications?
If you like the idea, please contribute to the Definition process. And if you don't, you're more than welcome to express that too :)
Showing posts with label RCP. Show all posts
Showing posts with label RCP. Show all posts
Thursday, June 17, 2010
Monday, February 1, 2010
Validating MDL SD files and Symyx molfiles with the CDK
Bioclipse 2.0 introduced a new, powerful molecular table support, and we have been eager to test that on large SD files. A recent ChEBI SD file failed to open, and eyes were immediately at the CDK, which is the cheminformatics library used in Bioclipse.
After careful investigations, it turned out that the ChEBI file contained a few entries which were not MDL molfiles, but queries for the ISISBase system. Those cannot be read by the CDK MDLV2000Reader. However, it crashed on it, instead of failing more savely. That's not nice, and fixed. But, the problem is rather recurrent, and the reason why I like CML so much: invalid input. CML, based on XML, has several general validation approaches that give in-depth error messages of what is wrong with the file.
So, I asked on the BOx what the Open Source cheminformatics community had to offer for this. Turns out that several tools find problems in the files, but none could report where the error occurred.
Validation
Now, some time ago, I played with two reading modes, RELAXED and STRICT, as faulty files is core cheminformatics material, and the software is blamed if the QSAR model resulting from it is not good (seriously). Anyways, a small API change in the CDK would make a validating MDLV2000Reader quite a step closer, but I had not followed up on it until last Friday where I patch I was reviewing caused 6 new unit test fails. The new fails were caused by a assumption which turned out the be false in the test files used in those 6 unit tests.
The MDL (or Symyx) molfile specifications (not an Open Specification) defines an atom block line as:
Now, personally, I rather send the file back to the user with a proper error report and show them what is wrong with the file. Or better, provide them with a MDL V2000 text editor (e.g. in Bioclipse) which would graphically highlight errors, as many of us are used to with Eclipse:
CDK Patch
So, I am hacking up a patch for CDK master to allow error reporting by IChemObjectReaders. The initial version of the API update and use in the MDLV2000Reader are available as Gist 290659. They are not final yet, as I realized when making the above screenshot, that merely int col is not enough, and that I actually need the startCol and endCol positions instead. Also, there are only an error level at this moment, and no warning level as in the screenshot.
That said, I created a jar (ant dist-large) and saved it as mdlCheck.jar, and wrote a bit of Groovy:
which defines a class implementing the new IChemObjectReaderErrorHandler and then reads a MDL molfile. And the output looks like it fulfills my needs:
Or, another common found issue (using D and T as element symbols):
Enough for now... dinner time.
After careful investigations, it turned out that the ChEBI file contained a few entries which were not MDL molfiles, but queries for the ISISBase system. Those cannot be read by the CDK MDLV2000Reader. However, it crashed on it, instead of failing more savely. That's not nice, and fixed. But, the problem is rather recurrent, and the reason why I like CML so much: invalid input. CML, based on XML, has several general validation approaches that give in-depth error messages of what is wrong with the file.
So, I asked on the BOx what the Open Source cheminformatics community had to offer for this. Turns out that several tools find problems in the files, but none could report where the error occurred.
Validation
Now, some time ago, I played with two reading modes, RELAXED and STRICT, as faulty files is core cheminformatics material, and the software is blamed if the QSAR model resulting from it is not good (seriously). Anyways, a small API change in the CDK would make a validating MDLV2000Reader quite a step closer, but I had not followed up on it until last Friday where I patch I was reviewing caused 6 new unit test fails. The new fails were caused by a assumption which turned out the be false in the test files used in those 6 unit tests.
The MDL (or Symyx) molfile specifications (not an Open Specification) defines an atom block line as:
xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneeebut does not specify which fields are optional. And indeed, many tools around save MDL molfiles with one or more fields missing, leading to shorter than expected line lengths. And, as you might have expected, the failing unit tests had files with lines missing the field introduced by the patch, causing Exceptions being thrown around. I have yet to make up my mind of the lack of those fields is a problem in the file, or allowed by the format. In either case, the information from that field is not available, and the reader could safely ignore the missing information. Per user demand.
Now, personally, I rather send the file back to the user with a proper error report and show them what is wrong with the file. Or better, provide them with a MDL V2000 text editor (e.g. in Bioclipse) which would graphically highlight errors, as many of us are used to with Eclipse:
CDK Patch
So, I am hacking up a patch for CDK master to allow error reporting by IChemObjectReaders. The initial version of the API update and use in the MDLV2000Reader are available as Gist 290659. They are not final yet, as I realized when making the above screenshot, that merely int col is not enough, and that I actually need the startCol and endCol positions instead. Also, there are only an error level at this moment, and no warning level as in the screenshot.
That said, I created a jar (ant dist-large) and saved it as mdlCheck.jar, and wrote a bit of Groovy:
which defines a class implementing the new IChemObjectReaderErrorHandler and then reads a MDL molfile. And the output looks like it fulfills my needs:
$ CLASSPATH=mdlCheck.jar groovy mdlCheck.groovy src/test/data/mdl/test6.sdf location: 5, 35: Could not parse mass difference field. -> For input string: "" location: 6, 35: Could not parse mass difference field. -> For input string: ""Note to myself, that atom block does not like like a MDL molfile atom block at all! Every second line outputs the Exception passed to the error handler. I have to say, those messages are rather cryptic, but resulting from a NumberFormatException, if not mistaken.
Or, another common found issue (using D and T as element symbols):
$ CLASSPATH=mdlCheck.jar groovy mdlCheck.groovy src/test/data/mdl/hisotopes.mol location: 6, 32: Invalid element type. Must be an existing element, or one in: A, Q, L, LP, *. location: 7, 32: Invalid element type. Must be an existing element, or one in: A, Q, L, LP, *.
Enough for now... dinner time.
Wednesday, December 16, 2009
Target Platform to have $HOME/.eclipse/$ECLIPSE/plugins ??
Bioclipse uses a custom target-platform... but since I am using the Eclipse 3.5 from Ubuntu now, extra features I download (GEF, BIRT, EMF, ...) end up in $HOME... so, I need to add a folder to the target-platform.target file... but I cannot find the variable for $HOME/.eclipse/org.eclipse.platform_3_foo_bar/plugins, such the files has things like @{eclipse_home}/plugins too...
Right now I have the below, but that clearly is not the solution:
What is the @{variable} I should use for user-based plugin folders?
Right now I have the below, but that clearly is not the solution:
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<?pde version="3.5"?>
<target name="Spring-osgi-1.0.2">
<locations>
<location path="${eclipse_home}" type="Profile"/>
<location path="${project_loc}/spring-osgi-1.0.2/dist" type="Directory"/>
<location path="${project_loc}/libs" type="Directory"/>
<location path="${project_loc}/spring-osgi-1.0.2/lib" type="Directory"/>
<location path="${eclipse_home}/plugins" type="Directory"/>
<location path="/home/egonw/.eclipse/org.eclipse.platform_3.5.0_155965261/plugins"
type="Directory"/>
</locations>
</target>
What is the @{variable} I should use for user-based plugin folders?
Wednesday, September 23, 2009
Extension point for running JUnit tests in a RCP Application instance?
One thing that has been on my wishlist is to be able to run the unit tests we have for Bioclipse from inside a running Bioclipse instance. That is, we have a Bioclipse Test Suite features on the update site, matching the functional features we have there. Each such test suite would run all JUnit tests we have for that feature.
The good thing about this is twofold:
So, my question is, did anyone set up an system like this? And, is there an extension point that allows features to plugin additional JUnit test suites into a larger test suite dynamically?
The good thing about this is twofold:
- users can verify that their installation is working as intended
- the development team can easily run the test suite on foreign systems, without the need to install a fully operational Eclipse with Bioclipse development workspace
So, my question is, did anyone set up an system like this? And, is there an extension point that allows features to plugin additional JUnit test suites into a larger test suite dynamically?
Saturday, January 3, 2009
Editing and Validation of CML documents in Bioclipse
One advantage of using XML is that one can rely on good support in libraries for functionality. When parsing XML, one does not have to take care of the syntax, and focus on the data and its semantics. This comes at the expense of verbosity, though, but having the ability to express semantics explicitly is a huge benefit for flexibility.
So, when Peter and Henry put their first documents online about the Chemical Markup Language (CML), I was thrilled, even though is actually was still SGML when I encountered it. The work predates the XML recommendation. As I recently blogged, in '99 I wrote patches for Jmol and JChemPaint to support CML, which were published as preprint in the Chemical Preprint Server in a paper in 2000 in the Internet Journal of Chemistry. Neither of the two has survived.
Anyway, the Chemistry Development Kit makes heavy use of CML, and Bioclipse supports it too. Now, Bioclipse is based on the Eclipse Rich Client Platform architecture, for which there exist quite a few XML tools in the Web Tools Platform (WTP). Among these, a validation, content assisting XML editor. This means, I get red markings when I make my XML document not-well-formed or invalid. Just a quick recap: well-formedness means that the XML document has a proper syntax: one root node, properly closed tags, quotes around attribute values, etc. Validness, however, means that the document is well-formed, but also hierarchically organized according to some specification.
Enter CML. CML is such a specification, first with DTDs, but after the introduction of XML Namespaces with XML Schema (see There can be only one (namespace)). The WTP can use this XML Schema for validation, and this is of great help learning the CML language. Pressing Ctrl-space in Bioclipse will now show you what allowed content can be added at the current character position.
Yes, Bioclipse can do this now (in SVN, at least). This has been on my wishlist for at least two years now, but never really found the right information. Now, three days ago David wrote about End of Year Cramps in which he describes some of his work on the WTP for autocomplete for XPath queries. He see[s] a brighter future for XML at eclipse over the next year. I hope that those in the eclipse and XML community will help to continue to improve the basic support, so that first class commercial quality applications that leverage this support can continue to be built.
That was enough statement for me to ask in the comments on how to make the WTP XML editor aware of the CML XML Schema. It already picked up XML Schema's with xsi:schemaLocation, but I needed something to worked without such statements in the XML document itself. David explained that me that I could use the org.eclipse.wst.xml.catalog extension. This was really easy, and commited to Bioclipse SVN as:
Therefore, I headed to #eclipse and actually met David of the blog that started this again. He asked nitind to think about it too, and they helped me pin down the issue. This relevant bit of the stacktrace turned out to be:
So, the plugin I turned to to have missing was org.eclipse.core.runtime.compatibility. Apparently, some parts of the WTP that the XMLEditor is using, still uses Eclipse2.x technology.
This screenshot shows the WTP XMLEditor in action in Bioclipse on a CML file. It shows the document contents with the 'Design' tab, which also shows allowed content, as derived from the XML Schema for CML. Also, note that the Outline and Properties view automatically come for free, which allows more detail and navigation of the content.
This screenshot shows the 'Source' tab for the same file, where I deliberately changed the value of the @id attribute of the first atom. The value does not validate against the regular expression defined in the CML schema for @id attribute values. It also shows the content assisting in action. At any location in the CML file, I can hit Ctrl-Space, and the editor will show me which content I can add at that location.
This makes Bioclipse a perfect tool to craft CML documents and learn the language.
So, when Peter and Henry put their first documents online about the Chemical Markup Language (CML), I was thrilled, even though is actually was still SGML when I encountered it. The work predates the XML recommendation. As I recently blogged, in '99 I wrote patches for Jmol and JChemPaint to support CML, which were published as preprint in the Chemical Preprint Server in a paper in 2000 in the Internet Journal of Chemistry. Neither of the two has survived.
Anyway, the Chemistry Development Kit makes heavy use of CML, and Bioclipse supports it too. Now, Bioclipse is based on the Eclipse Rich Client Platform architecture, for which there exist quite a few XML tools in the Web Tools Platform (WTP). Among these, a validation, content assisting XML editor. This means, I get red markings when I make my XML document not-well-formed or invalid. Just a quick recap: well-formedness means that the XML document has a proper syntax: one root node, properly closed tags, quotes around attribute values, etc. Validness, however, means that the document is well-formed, but also hierarchically organized according to some specification.
Enter CML. CML is such a specification, first with DTDs, but after the introduction of XML Namespaces with XML Schema (see There can be only one (namespace)). The WTP can use this XML Schema for validation, and this is of great help learning the CML language. Pressing Ctrl-space in Bioclipse will now show you what allowed content can be added at the current character position.
Yes, Bioclipse can do this now (in SVN, at least). This has been on my wishlist for at least two years now, but never really found the right information. Now, three days ago David wrote about End of Year Cramps in which he describes some of his work on the WTP for autocomplete for XPath queries. He see[s] a brighter future for XML at eclipse over the next year. I hope that those in the eclipse and XML community will help to continue to improve the basic support, so that first class commercial quality applications that leverage this support can continue to be built.
That was enough statement for me to ask in the comments on how to make the WTP XML editor aware of the CML XML Schema. It already picked up XML Schema's with xsi:schemaLocation, but I needed something to worked without such statements in the XML document itself. David explained that me that I could use the org.eclipse.wst.xml.catalog extension. This was really easy, and commited to Bioclipse SVN as:
<extensionHowever, that does not make the WTP XML editor available in the Bioclipse application yet. Not ever in the "Open With"... So, I set up a CML Feature. After a follow up question, it turned out that the CML content type of Bioclipse was already a sub type of the XML type (see ):
point="org.eclipse.wst.xml.core.catalogContributions">
<catalogContribution>
<uri name="http://www.xml-cml.org/schema"
uri="schema24/schema.xsd"/>
</catalogContribution>
</extension>
<extensionSo, the only remaining problem was to actually get the WTP XML editor as part of the Bioclipse application. The new CML Feature takes care of that (I hope the export and building the update site work too, but that's yet untested), by important the relevant plugins and features. Last night, however, I ended up with one stacktrace which gave me little clue on which plugin I was still missing.
point="org.eclipse.core.runtime.contentTypes">
<content-type
base-type="org.eclipse.core.runtime.xml"
id="net.bioclipse.contenttypes.cml"
name="Chemical Markup Language (CML)"
file-extensions="cml,xml"
priority="normal">
</content-type>
</extension>
Therefore, I headed to #eclipse and actually met David of the blog that started this again. He asked nitind to think about it too, and they helped me pin down the issue. This relevant bit of the stacktrace turned out to be:
Caused by: java.lang.IllegalStateExceptionThis refered to this bit of code of Eclipse' Platform.java:
at org.eclipse.core.runtime.Platform.getPluginRegistry(Platform.java:774)
at org.eclipse.wst.common.componentcore.internal.impl.WTPResourceFactoryRegistry$ResourceFactoryRegistryReader.(WTPResourceFactoryRegistry.java:275)
at org.eclipse.wst.common.componentcore.internal.impl.WTPResourceFactoryRegistry.(WTPResourceFactoryRegistry.java:61)
at org.eclipse.wst.common.componentcore.internal.impl.WTPResourceFactoryRegistry.(WTPResourceFactoryRegistry.java:55)
... 37 more
Bundle compatibility = InternalPlatform.getDefault()
.getBundle(CompatibilityHelper.PI_RUNTIME_COMPATIBILITY);
if (compatibility == null)
throw new IllegalStateException();
So, the plugin I turned to to have missing was org.eclipse.core.runtime.compatibility. Apparently, some parts of the WTP that the XMLEditor is using, still uses Eclipse2.x technology.
This screenshot shows the WTP XMLEditor in action in Bioclipse on a CML file. It shows the document contents with the 'Design' tab, which also shows allowed content, as derived from the XML Schema for CML. Also, note that the Outline and Properties view automatically come for free, which allows more detail and navigation of the content.
This screenshot shows the 'Source' tab for the same file, where I deliberately changed the value of the @id attribute of the first atom. The value does not validate against the regular expression defined in the CML schema for @id attribute values. It also shows the content assisting in action. At any location in the CML file, I can hit Ctrl-Space, and the editor will show me which content I can add at that location.This makes Bioclipse a perfect tool to craft CML documents and learn the language.
A RCP dedicated blog
Yes, yet another blog by me. This one is special, being the first where I just copy/paste blog items from other blog I do. Just, so that people only interested in RCP related stuff, can tune in here. If only I knew how to do categories on blogger.com.
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